Transcriptional profiling of microglia; current state of the art and future perspectives
Open accessAbstract
Microglia are the tissue macrophages of the central nervous system (CNS) and the first to respond to CNS dysfunction and disease. Gene expression profiling of microglia during development, under homeostatic conditions, and in the diseased CNS provided insight in microglia functions and changes thereof. Single‐cell sequencing studies further contributed to our understanding of microglia heterogeneity in relation to age, sex, and CNS disease. Recently, single nucleus gene expression profiling was performed on (frozen) CNS tissue. Transcriptomic profiling of CNS tissues by (single) nucleus RNA‐sequencing has the advantage that it can be applied to archived and well‐stratified frozen specimens. Here, we give an overview of the significant advances recently made in microglia transcriptional profiling. In addition, we present matched cellular and nuclear microglia RNA‐seq datasets we generated from mouse and human CNS tissue to compare cellular versus nuclear transcriptomes from fresh and frozen samples. We demonstrate that microglia can be similarly profiled with cell and nucleus profiling, and importantly also with nuclei isolated from frozen tissue. Nuclear microglia transcriptomes are a reliable proxy for cellular transcriptomes. Importantly, lipopolysaccharide‐induced changes in gene expression were conserved in the nuclear transcriptome. In addition, heterogeneity in microglia observed in fresh samples was similarly detected in frozen nuclei of the same donor. Together, these results show that microglia nuclear RNAs obtained from frozen CNS tissue are a reliable proxy for microglia gene expression and cellular heterogeneity and may prove an effective strategy to study of the role of microglia in neuropathology.
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Genes upregulated by LPS stimulation in mice are depleted in nuclei.
“Genes upregulated by lipopolysaccharide (LPS) stimulation in mice (Gerrits et al., 2019) also showed depletion in nuclei (NES = −1.86, padj = 3.6e-05; Figure 2C; Figure S2F).”
From Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans (2020) · cites this paper as Gerrits et al., 2019
Genes defined by Gerrits et al. as cellular enriched in microglial cells versus fresh nuclei in humans were also enriched in cells in our data.
“Finally, the genes defined by Gerrits et al. (2019) as cellular enriched in a differential analysis of microglial cells versus (fresh) nuclei in humans were also enriched in cells in our data, showing a NES score of −1.92 (padj = 3.6e-05).”
From Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans (2020) · cites this paper as Gerrits et al., 2019
In agreement with Gerrits et al., fresh nuclei versus cells showed very little difference.
“In agreement with the results of Gerrits et al. (2019), when we plotted the normalized abundance of fresh nuclei versus cells, we saw very little difference between the two populations (Figure S3C).”
From Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans (2020) · cites this paper as Gerrits et al., 2019
When comparing frozen nuclei to fresh cells from Gerrits et al., the same set of nuclei-depleted genes showed lower relative abundance in frozen nuclei.
“However, when we compared frozen nuclei to fresh cells, we again observed the same set of nuclei-depleted genes showing a lower relative abundance in frozen nuclei of Gerrits et al. (2019) (Figure S3D).”
From Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans (2020) · cites this paper as Gerrits et al., 2019
Single-cell RNA sequencing has revealed significant functional heterogeneity among microglial subtypes and their inflammatory profiles in the neurodegenerative setting.
“single-cell RNA sequencing, which enables the profiling of individual microglial cells with high-throughput datasets, has revealed significant functional heterogeneity among microglial subtypes and their inflammatory profiles in the neurodegenerative setting [109, 119].”
From Systems-based proteomics to resolve the biology of Alzheimer’s disease beyond amyloid and tau (2021) · cites this paper as [119]
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- Authors
- Gerrits, E., Heng, Y., Boddeke, E. W. G. M., & Eggen, B. J. L.
- Affiliations
- University Medical Center Groningen (NL)
- Corresponding author
- Eggen, Bart J. L.
- Venue
- Glia
- Publisher
- Wiley
- Published
- 2019-12-17
- Volume
- 68
- Issue
- 4
- Pages
- 740-755
- ISSN
- 0894-1491 (ISSN-L)
- 1098-1136
- PMC
- PMC7064956
- OpenAlex
- W2994850755
- Cited by
- 140
- References
- 51
- Citations by year
- 2026: 17 · 2025: 23 · 2024: 17 · 2023: 16 · 2022: 22 · 2021: 29 · 2020: 16
- FWCI
- 1.80
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Glia (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
- Funders
- China Scholarship Council
- Universitair Medisch Centrum Groningen
- Topics
- Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Health Sciences › Medicine › Pathology and Forensic Medicine › Multiple Sclerosis Research Studies
- Keywords
- microglia, gene expression profiling, single-nucleus RNA sequencing, single-cell RNA sequencing, microglial heterogeneity, nuclear transcriptome, lipopolysaccharide response, neuropathology
- MeSH terms
- Animals, Cell Nucleus, Humans, Sequence Analysis, RNA, Microglia, Gene Expression Profiling, Mice, Transcriptome
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Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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